I have a character creation session coming up soon for a new campaign that I'll be GM'ing, so I've been compiling some notes to help the new players through the process. From memory, I put down that Obligation and Motivation are chosen together during Step 2, but going back through the book I see that Motivation comes near the very end.

It may just be a guideline, but is there a reason to push Motivation that far towards the end? I'd think you'd want to nail it down when you select Obligation so you have your whole concept before choosing Career, Specs, Skills, etc. Would there be any problems with doing it that way that I'm overlooking?

The concept should be developed up front, but after that it doesn't matter. The order of steps in the character creation process is a guideline. The only thing that must be done in order is determining the Derived Attributes at the very end (WT, ST, Soak). A player can even change duty/motivation to fit the concept better if required as he goes along.

It may just be a guideline, but is there a reason to push Motivation that far towards the end? I'd think you'd want to nail it down when you select Obligation so you have your whole concept before choosing Career, Specs, Skills, etc. Would there be any problems with doing it that way that I'm overlooking?

The primary reason, I think, is because Motivation is much less important to the mechanics of the game, and so can be rather freely added onto any character you might make, while your choice of Obligation may inform your Career choice. However, both Obligation and Motivation are about equal when it comes to the narrative aspect of the game.

But Domingo is right, the whole thing is just a guideline. If you wanted to, you could pair Obligation and Motivation together and move from that into selecting Career or what-have-you.